4-31943027-C-T

Variant names:

• chr4-31943027-C-T
• rs4446365

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.147 in 152,020 control chromosomes in the GnomAD database, including 1,969 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22357 AN: 151902 Hom.: 1966 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.166

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.147 AC: 22384 AN: 152020 Hom.: 1969 Cov.: 32 AF XY: 0.150 AC XY: 11115 AN XY: 74278

African (AFR) AF: 0.108 AC: 4480 AN: 41488

American (AMR) AF: 0.289 AC: 4411 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 397 AN: 3466

East Asian (EAS) AF: 0.124 AC: 639 AN: 5164

South Asian (SAS) AF: 0.212 AC: 1023 AN: 4820

European-Finnish (FIN) AF: 0.120 AC: 1268 AN: 10542

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9642 AN: 67968

Other (OTH) AF: 0.169 AC: 358 AN: 2114

Alfa AF: 0.144 Hom.: 2021

Bravo AF: 0.157

Asia WGS AF: 0.201 AC: 700 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.33
PhyloP100		-0.036

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4446365; hg19: chr4-31944649;